The lawmakers, who rejected Yuriy Yekhanurov on Tuesday, this time gave him 289 votes - well above the 226 he needed.
The extra backing came after Yushchenko signed a formal truce with the Party of the Regions, led by losing presidential candidate Viktor Yanukovych. That support helped Yushchenko offset the defection of some of his Orange Revolution allies after the ouster of former Prime Minister Yulia Tymoshenko.
With only six months until key parliamentary elections, the move puts Yushchenko in the uncomfortable position of having to justify his truce with the political forces he opposed last year.
"It's time to bury the war hatchet and to forget where it lies," Yushchenko said before the vote. Later, he said a "unique understanding" had been found.
After the vote, deputies applauded as Yushchenko warmly hugged Yekhanurov.
Yekhanurov, a Russian-born former governor from eastern Ukraine, said he would unveil his Cabinet next week. He said at least a third of his appointments would be technocrats with no relation to politics.
The deal was tailored to give greater rights to the opposition and pushes forward implementation of reforms that would strip the president of most of his powers in favor of parliament. It also gives more power to local authorities, including immunity from prosecution for deputies in regional parliaments.
Yushchenko dismissed Tymoshenko and her government Sept. 8 as his circle of Orange Revolution allies who brought him to power disintegrated amid mutual allegations of corruption and infighting.